Chapter 10 Gut microbiota: functional analysis

10.1 MCI

GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) %>%
#  filter(time_point=="0_Wild") %>%
  group_by(environment) %>%
  summarise(MCI = mean(value), sd = sd(value))
# A tibble: 2 × 3
  environment   MCI     sd
  <fct>       <dbl>  <dbl>
1 low         0.321 0.0149
2 high        0.298 0.0288
MCI <- GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) 
# %>% 
#   filter(diet!="Post_grass")

shapiro.test(MCI$value)

    Shapiro-Wilk normality test

data:  MCI$value
W = 0.78617, p-value = 3.708e-05
wilcox.test(value ~ environment, data=MCI)

    Wilcoxon rank sum exact test

data:  value by environment
W = 184, p-value = 0.002306
alternative hypothesis: true location shift is not equal to 0

10.2 Wilcoxon

10.2.1 Community elements differences:

   Elements          low        high                                        Function
1     B0205 0.6215078000 0.556359700               Amino acid biosynthesis_Threonine
2     B0208 0.7210440000 0.636853500                  Amino acid biosynthesis_Valine
3     B0211 0.7945017000 0.725047800                  Amino acid biosynthesis_Lysine
4     B0212 0.6037965000 0.534577500                Amino acid biosynthesis_Arginine
5     B0216 0.5185759000 0.403716800              Amino acid biosynthesis_Tryptophan
6     B0217 0.4350579000 0.386313200           Amino acid biosynthesis_Phenylalanine
7     B0303 0.2366397000 0.210934100      Amino acid derivative biosynthesis_Ectoine
8     B0309 0.0982039000 0.080454810   Amino acid derivative biosynthesis_Putrescine
9     B0310 0.0074509910 0.001588408   Amino acid derivative biosynthesis_Tryptamine
10    B0403 0.5460416000 0.526315000                    SCFA biosynthesis_Propionate
11    B0602 0.7980851000 0.748664900             Organic anion biosynthesis_Fumarate
12    B0710 0.1077906000 0.069865730         Vitamin biosynthesis_Phylloquinone (K1)
13    B0805 0.2209180000 0.163027300 Aromatic compound biosynthesis_Indole-3-acetate
14    B1014 0.0002108536 0.002070099              Antibiotic biosynthesis_Kanosamine
15    D0104 0.1621682000 0.121988700            Lipid degradation_Dicarboxylic acids
16    D0204 0.4792235000 0.412658000               Polysaccharide degradation_Chitin
17    D0206 0.5883225000 0.484839300       Polysaccharide degradation_Alpha galactan
18    D0210 0.3375139000 0.277216900          Polysaccharide degradation_Beta-mannan
19    D0213 0.3703334000 0.300628500                Polysaccharide degradation_Mucin
20    D0302 0.1295141100 0.087387210                       Sugar degradation_Sucrose
21    D0310 0.4599834000 0.385078900                         Sugar degradation_NeuAc
22    D0603 0.0174939660 0.004478505             Nitrogen compound degradation_Urate
23    D0606 0.0327311000 0.019533340         Nitrogen compound degradation_Allantoin
24    D0704 0.4279568000 0.338026300                    Alcohol degradation_Glycerol
25    D0807 0.0550681500 0.028201350                 Xenobiotic degradation_Catechol
26    D0816 0.1240800200 0.098151990            Xenobiotic degradation_Phenylacetate
27    D0817 0.0139664790 0.008498965          Xenobiotic degradation_Trans-cinnamate
28    S0104 0.2384995000 0.206859100            Cellular structure_Lipoteichoic acid

10.2.2 Community functions differences

  Code_function        low       high                       Function
1           B02 0.57566870 0.52445070        Amino acid biosynthesis
2           B08 0.45983730 0.42094060 Aromatic compound biosynthesis
3           D08 0.02386816 0.01341748         Xenobiotic degradation

10.2.3 Community domains differences

   Code_domain       low      high
1 Biosynthesis 0.4097942 0.3885795
2  Degradation 0.2194927 0.1947749